I had an Idea of a setting called layers, layers are a way to make it so that certain objects can pass through eachother and still be effected with gravity without falling through the floor into oblivion, then you can select the objects so that they either exist on layer 1, 2, 3 or all, and then have another object setting that you can mark whether its visible on all layers or just that layer.
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Collision by layer option would definitely be nice.